Pod 5 subsets

[Jeff-Field]

Does this program allow one to search out reads of interest, organize them and then work again with them? For example, when i am interested in a subset of reads, eg those for my favorite gene, or the ones with the highest quality scores, can i pull just those reads from a large data set into a smaller one so that I can baseball them again, or work with them in other programs? If this is not the best program, does another program, perhaps HDF5 allow pod5 file organizing and filtering ?

[HalfPhoton]

Hi @Jeff-Field , yes you are able to do this with the pod5 tools.

Subset is best suited for the use case where you want to create multiple output files from some inputs using some other metadata such as genome. We can write a new pod5 file per genome which contains only reads matching that genome for example.

The documentation has some examples of this:

https://pod5-file-format.readthedocs.io/en/latest/docs/tools.html#pod5-subset

There is a simpler tool filter which takes a list of read IDs and copies only those reads into a new output. If that's more suitable for your workflow

https://pod5-file-format.readthedocs.io/en/latest/docs/tools.html#pod5-filter

Kind regards,
Rich